4DZ4A

X-ray crystal structure of a hypothetical agmatinase from burkholderia thailandensis
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 119
Slipknot S +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 30-167 138 1-27, 279-316 28-29, 168-278 27 38 slipknot
Chain Sequence
TLYGDGAIRRPSVYGSSIENTYAGVLSFMRRNYTRDLDGVDVVVSGVPLDLATTFRSGARLGPSAVRAASVQLAELNPYPWGFDPFDDLAVIDYGDCWFDAHHPLSIKPAIVEHARTILQSDARMLTLGGDHYITYPLLIAHAQKYGKPLSLIHFDAHCDTWAD---DSLNHGTMFYKAVKDGLIDPKASVQVGIRTWNDDYLGINVLDAAWVHEHGARATLERIESIVGGRPAYLTFDIDCLDPAFAPGTGTPVAGGLSSAQALAIVRGLGGVNLIGADVVEVAPAYDQSEITAIAAAHVACDLLCLWRQRKAGA
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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2.1 32-237 206 1-25, 253-313 26-31, 238-252 25 61 slipknot
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2.1 32-97 66 1-26, 124-313 27-31, 98-123 26 190 slipknot
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2.1 32-159 128 1-26, 181-313 27-31, 160-180 26 133 slipknot
sequence length 316
structure length 313
publication title Combining functional and structural genomics to sample the essential Burkholderia structome.
pubmed doi rcsb
molecule tags Hydrolase
molecule keywords Agmatinase
source organism Burkholderia thailandensis
missing residues 165-167
total genus Genus: 119
ec nomenclature ec 3.5.3.11: Agmatinase.
pdb deposition date 2012-02-29
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00491 Arginase Arginase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.800.10 Alpha Beta 3-Layer(aba) Sandwich Arginase; Chain A Arginase; Chain A 4dz4A00
1WOHA 1GQ7A 1GQ6A 4DZ4A 1WOGA 1WOIA
chains in the KnotProt database with same CATH superfamily
1WOHA 1GQ7A 1GQ6A 4DZ4A 1WOGA 1WOIA
chains in the KnotProt database with same CATH topology
1WOHA 1GQ7A 1GQ6A 4DZ4A 1WOGA 1WOIA
chains in the KnotProt database with same CATH homology

  
#chains in the KnotProt database with same CATH superfamily
 1WOH A;  1GQ7 A;  1GQ6 A;  4DZ4 A;  1WOG A;  1WOI A; 
#chains in the KnotProt database with same CATH topology
 1WOH A;  1GQ7 A;  1GQ6 A;  4DZ4 A;  1WOG A;  1WOI A; 
#chains in the KnotProt database with same CATH homology
 1WOH A;  1GQ7 A;  1GQ6 A;  4DZ4 A;  1WOG A;  1WOI A;
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling